In this study, we want to find out the relationship between the bridge natural frequency and the bridge foundation scour depth. The Improved Ibrahim Time Domain (IITD) method and the finite element models are applied to solve the problem. Firstly, IITD method was described in detail for using to solve the natural frequency at ambient excitation. Secondly, the detailed steps of expiring the relationship between bridge natural frequencies and foundation scour depth are explained using IITD method and finite element techniques. Finally, the natural frequency of Qujiang Bridge is calculated at different scour depth. The detailed analysis of the natural frequency of the bridge with the variation of scour depth can able to explore the impact of bridge scour damage for structural safe operation. The results of calculated showed the IITD method that considered the ambient excitation is much more powerful and accurate than Irahim Time Domain (ITD) method. So IITD can apply to bridge scour damage detection with finite element techniques. This study laid the foundation for the bridge scour identification.